{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0310XYPS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0310XYPS",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR1_Rep1_S115",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR1_Rep2_S170",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR2_Rep1_S121",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR2_Rep2_S176",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR3_Rep1_S127",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR3_Rep2_S182",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR4_Rep1_S133",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR4_Rep2_S188"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2394VMWJ](/auxiliary-sets/IGVFDS2394VMWJ/) has sequence file(s) [IGVFFI4083RNOM](/sequence-files/IGVFFI4083RNOM/), [IGVFFI6531JUDM](/sequence-files/IGVFFI6531JUDM/), [IGVFFI0145XWMG](/sequence-files/IGVFFI0145XWMG/), [IGVFFI1648DHDD](/sequence-files/IGVFFI1648DHDD/), [IGVFFI6318MDEU](/sequence-files/IGVFFI6318MDEU/), [IGVFFI3208UFEI](/sequence-files/IGVFFI3208UFEI/), [IGVFFI3894LVNC](/sequence-files/IGVFFI3894LVNC/), [IGVFFI1771JOTI](/sequence-files/IGVFFI1771JOTI/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS2394VMWJ/"
}
],
"WARNING": [
{
"category": "missing files",
"detail": "Measurement set [IGVFDS0310XYPS](/measurement-sets/IGVFDS0310XYPS/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/measurement-sets/IGVFDS0310XYPS/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9055BZJI/",
"accession": "IGVFDS9055BZJI",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_MYC-Auxin6hrs-FF1"
],
"file_set_type": "cell sorting",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS2394VMWJ/",
"accession": "IGVFDS2394VMWJ",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR1_Rep1_S115",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR1_Rep2_S170",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR2_Rep1_S121",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR2_Rep2_S176",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR3_Rep1_S127",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR3_Rep2_S182",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR4_Rep1_S133",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR4_Rep2_S188"
],
"file_set_type": "gRNA sequencing",
"status": "released"
}
],
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_for": [],
"creation_timestamp": "2024-05-21T17:35:01.083227+00:00",
"documents": [
"/documents/74d53b9c-ab1d-42e3-b679-d3a00ae3d842/"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [],
"input_for": [
"/analysis-sets/IGVFDS4544YEQM/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
"preferred_assay_title": "CRISPR FlowFISH screen",
"protocols": [
"https://www.protocols.io/view/crispri-of-regulatory-elements-upon-degron-operati-5jyl82d59l2w/v1"
],
"release_timestamp": "2024-07-10T19:48:09.424746+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0264XNND/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0264XNND",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR1_Rep1_S115",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR1_Rep2_S170",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR2_Rep1_S121",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR2_Rep2_S176",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR3_Rep1_S127",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR3_Rep2_S182",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR4_Rep1_S133",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinE-PCR4_Rep2_S188"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS7857SYCK/",
"accession": "IGVFDS7857SYCK",
"file_set_type": "guide library",
"status": "released",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"status": "released"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin E for 80-90% expression of MYC) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"status": "released",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T02:03:48.475864+00:00",
"summary": "mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"targeted_genes": [
{
"@id": "/genes/ENSG00000136997/",
"geneid": "ENSG00000136997",
"name": "MYC proto-oncogene, bHLH transcription factor",
"status": "released",
"symbol": "MYC",
"synonyms": [
"bHLHe39",
"v-myc myelocytomatosis viral oncogene homolog",
"myc proto-oncogene protein",
"avian myelocytomatosis viral oncogene homolog",
"v-myc avian myelocytomatosis viral oncogene homolog",
"transcription factor p64",
"MRTL",
"c-Myc",
"myc-related translation/localization regulatory factor",
"MYCC",
"class E basic helix-loop-helix protein 39",
"proto-oncogene c-Myc"
]
}
],
"uuid": "18fc0fa7-09d6-4742-b38d-4660b70af27b"
}